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somatic_sniper.xml
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somatic_sniper.xml
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<tool id="somatic_sniper" name="Somatic Sniper" version="1.0.5">
<description> identify single nucleotide positions that are different between tumor and normal</description>
<requirements>
<container type="docker">somatic-sniper:1.0.5</container>
</requirements>
<command interpreter="python">SomaticSniper.py
$tumor
$normal
mutations.vcf
-f $reference
-t $tumor_name
-n $normal_name
-F vcf
#if $mapq
-q $mapq
#end if
#if $somaticq
-Q $somaticq
#end if
#if $loh
-L
#end if
#if $gor
-G
#end if
#if $dis_priors
-p
#end if
#if $use_priorp
-J
#end if
#if $prior_p
-s $prior_p
#end if
--workdir ./
</command>
<inputs>
<param name="tumor" type="data" format="bam" label="TumorBAM" />
<param name="normal" type="data" format="bam" label="NormalBAM" />
<param name="reference" type="data" format="fasta" label="Reference sequence in FASTA format"/>
<param name="tumor_name" type="text" value="TUMOR" label="Tumor sample id (for VCF header)" />
<param name="normal_name" type="text" value="NORMAL" label="Normal sample id (for VCF header)" />
<param name="mapq" type="integer" value="0" optional="true" label="Filter reads with mapping quality less than"/>
<param name="somaticq" type="integer" value="15" optional="true" label="Filter snv output with quality less than"/>
<param name="loh" type="boolean" optional="true" label="Do not report LOH variants as determined by genotypes" />
<param name="gor" type="boolean" optional="true" label="Do not report Gain of Reference variants as determined by genotypes" />
<param name="dis_priors" type="boolean" optional="true" label="Disable priors in the somatic calculation" />
<param name="use_priorp" type="boolean" optional="true" label="Prior probabilities accounting for somatic mutation rate" />
<param name="prior_p" type="float" optional="true" value="0.01" label="Prior probability of a somatic mutation" />
</inputs>
<outputs>
<data format="vcf" name="output" label="Somatic_Sniper.vcf" from_work_dir="mutations.vcf"/>
</outputs>
<stdio>
<exit_code range="1:" level="fatal" />
</stdio>
<help>
|
**Reference**
http://gmt.genome.wustl.edu/somatic-sniper/current/
-----
**What it does**
The purpose of this program is to identify single nucleotide positions that are different between tumor and normal
(or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the
differences. It outputs a file in a format very similar to Samtools consensus format. It uses the genotype likelihood
model of MAQ (as implemented in Samtools) and then calculates the probability that the tumor and normal genotypes are
different. This probability is reported as a somatic score. The somatic score is the Phred-scaled probability (between 0 to 255)
that the Tumor and Normal genotypes are not different where 0 means there is no probability that the genotypes are different and
255 means there is a probability of 1 – 10(255/-10) that the genotypes are different between tumor and normal. This is consistent
with how the SAM format reports such probabilities.
Bam files must contain LB tag in @RG line.
Picard tools can be used to add lines to BAM headers.
-----
**Input**
Tumor Sample:
bam tumor sample
Normal Sample:
bam normal sample
Reference Genome:
Fasta file of ref gnome
-----
**Options**
::
-q INT filtering reads with mapping quality less than INT [0]
-Q INT filtering somatic snv output with somatic quality less than INT [15]
-L FLAG do not report LOH variants as determined by genotypes
-G FLAG do not report Gain of Reference variants as determined by genotypes
-p FLAG disable priors in the somatic calculation. Increases sensitivity for solid tumors
-J FLAG Use prior probabilities accounting for the somatic mutation rate
-s FLOAT prior probability of a somatic mutation (implies -J) [0.010000]
-T FLOAT theta in maq consensus calling model (for -c/-g) [0.850000]
-N INT number of haplotypes in the sample (for -c/-g) [2]
-r FLOAT prior of a difference between two haplotypes (for -c/-g) [0.001000]
-n STRING normal sample id (for VCF header) [NORMAL]
-t STRING tumor sample id (for VCF header) [TUMOR]
-----
**Output**
Output file will be in VCF format.
</help>
</tool>